yes there is a way of running C++ on the Android-Emulator ( have a look here
C++ and JAVA syntax are almost the same,so it is your choice
I would (do) prefer JAVA, because it is about 10^10 times nicer and more comfortable to code than C++
Wont open and wounds here
The SDK on your pc is just a folder you unzip the downloaded SDK to. As you only have to referr to it in the Eclipse-Preferences there should be no problem.
Also Eclipse should not be worried if you move or reinstall it, as the settings ( not the plugins(like ADT), be their settings too
) are saved somewhere
like in the "C:/user/<loginname>/Local_Data/Eclipse
". The Emulator-Image is also saved in a folder on 'C:' ( C:UsersplusminusAppDataLocalAndroiduserdata.img).